Choices
by LMXB
Summary: As Cadmus returns Lena is forced into making a series of choices. Each could have lasting ramifications on her relationships with Kara, James, Alex and co.
1. Chapter 1

**Disclaimer** : I don't own Supergirl or the characters. This is written purely for fun.

 **A/N:** This is a short story (only a few chapters long) set after the end of Season 3. It will be angsty.

 **Synopsis** : As Cadmus returns Lena is forced into making a series of choices. Each could have lasting ramifications on her relationships with Kara, James, Alex and co.

* * *

"Something on your mind?" James asked as he moved onto the CatCo balcony where Lena was standing looking out over the city.

"Unfortunately." Lena replied.

"What's wrong?" He asked concerned.

"My mother made contact."

"Your mother? What did she want?" He questioned, moving to her side.

"To meet."

"You need to call the police."

"I can't. She said if I involved the police innocent people would die." Lena explained.

"So what are you going to do?"

"I have no choice. If I don't go innocent people will also die." Lena said.

"Did she give you any indication what she wants?"

"No." Lena said.

"But?" James asked sensing she was hiding something.

"But...someone hacked into L-Corp two weeks ago."

"What did they steal?"

"Research. We are still trying to figure out what."

"Why didn't you say anything?" James asked.

"We get attacks all the time. It was only this morning that my security team figured out how deep the attack went." Lena explained.

"But you think your mother is involved?"

"It seems too big a coincidence if she wasn't."

"Even more reason to get help." James pointed out.

"I can't. My family is responsible for too many deaths as it is. I won't be responsible for more."

"You can't go alone."

"Yes I can."

"I'll go with you, as Guardian. She didn't say you couldn't include me."

"I don't want you involved in that part of my life." Lena said.

"Being in a relationship means being involved in everything." James said.

"It's too risky." Lena said. "I have to do this alone." She added as Eve knocked on the balcony to door.

"Sorry to interrupt, but your ten o'clock is here."

-00-

"Kara can we talk?" James asked as he approached her desk that afternoon.

"Sure."

"Outside?" James asked.

"Um, okay." Kara said following him to his office then out onto the balcony. "What's up?"

"Lena."

"Is she okay?" Kara asked frowning.

"Her mother made contact. She wants to meet." He explained.

"Why? When? Has she told the police?" Kara asked sharing his concern.

"No idea, don't know and no." James said. "Lillian threatened to kill innocent people if she contacted the police, same if she doesn't turn up."

"So she's going alone?"

"Not if we can help it." James said. "I'm going to follow her, I was hoping you'd back me up."

"I'll be by her side." Kara said.

"She may not appreciate that."

"She already dislikes Supergirl." Kara reminded him.

-00-

As Kara sat in her apartment that evening waiting for James to make contact she finally built up the courage to make the call she had been avoiding. Picking up her phone she hit the speed dial and was half relieved when the call went straight to voice mail. Waiting for the beep she considered what she would say before taking a breath and saying.

"Hey Alex, I hope the meeting went well and you get home soon. I don't want you to stress but Lillian is back." As her phone buzzed she guessed James was calling and added. "..oh, I have to go. Call me when you land. Love you." With that she ended the call, changed into Supergirl and flew off to meet James and Lena.

-00-

"What are you doing here?" Lena asked as Supergirl landed next to her.

"I thought you might need back up."

"I don't need your help, we're not-"

"Friends." Supergirl finished for her. "I know, you told me. But that doesn't mean you don't need help."

"Let me guess, James told you." Lena said.

"He's worried about you. So am I."

"If my mother is going to show herself something tells me your presence won't help the situation." Lena pointed out.

"On the contrary it is exactly what I want." Lillian said stepping out of the shadows as Supergirl dropped to her knees, three green darts sticking out of her.

"What are you doing?" Lena asked.

"That is the wrong question." Lillian said as her team snapped Kryptonite cuffs on Supergirl. "The question is, what are we doing?"

 **-TBC...**

* * *

 **A/N:** Thanks for reading and reviewing.


	2. Chapter 2

**A/N:** Thanks for your comments. Sorry I didn't get this up sooner, I got stuck at an airport watching my flights getting delayed, cancelled, re-booked, delayed..

Guest (1) - Out of the main characters in this my current thinking is two relationships will be destroyed. One will be strengthened and the other still to be determined.

Chloe - Winn won't be in this, but Brainy will be working it.

Guest (2) - Hopefully it won't disappoint.

Alliedstatis - Lillian will be firmly in control of everything...

* * *

"Where is she?" Alex asked rushing into the DEO.

"Who?" Brainy asked.

"Kara." Alex said loosing patience.

"I don't know. She has not been in this morning. Have you tried calling her?" He answered before seeing the glare Alex was giving him. "I could attempt to trace her." He said quickly turning to his screen. "Strange, there have been no Supergirl sightings since last night."

"And you are only just noticing this now?" Alex ground out.

"I didn't think I was meant to be continually tracking her looking for anomalies." Brainy said.

"Of course you are. Our job is to keep her safe." Alex replied. "What can you tell me about the Lillian Luthor investigation?"

"What investigation?" Brainy asked.

"The one Kara asked you to do." Alex said, her anger growing almost as fast as her concern.

"She asked no such thing." Brainy replied.

"So you didn't know Lillian Luthor was back?" Alex asked, her panicking deepening.

"That is correct." Brainy confirmed.

"Damn it Kara, what have you done." Alex muttered before taking a deep breath and raising her voice.

"Listen up. I have reason to believe that Cadmus are around and they have Supergirl. I want everyone to work on finding them." With that she turned to leave.

"Where are you going and shouldn't you have a protection detail?" Brainy asked.

"Don't need one. I'm going to find Kara." With that she started to walk out of the control room.

"Director Danvers." Vasquez called.

"You've found her?" Alex asked hopefully.

"No ma'am. But I have scanned the hospital admissions and a man fitting James Olsen's description, including the Guardian suit, was admitted a couple of hours ago."

"Send me the details I'll go talk to him." Alex said rushing out.

-00-

As Lena came to she slowly sat up. Seeing her mother standing nearby she asked.

"What did you do to me?"

"You were not being cooperative so we had to sedate you." Lillian explained as Lena tried to recall what had happened.

"Supergirl?" Lena asked recalling events.

"Just through there." She said pointing to a clear tank where Supergirl sat on the floor.

"Why isn't she breaking out?" Lena asked concerned.

"Red light. It has neutralised her powers." Lillian smiled. "Now you are awake we can begin."

"Begin what?" Lena asked.

"The reason you are here. Avenging your brother. Something we can do because of you."

"What do you mean?" Lena asked.

"Perhaps we should let Supergirl be part of this discussion." Lillian said flicking a switch. "Don't look so bored." She said into a microphone. Looking up Kara saw Lena and jumped to her feet.

"Lena? Are you okay?"

"How touching." Lillian sneered. "So concerned about the woman who betrayed you, whose brilliance and ability has allowed this to happen."

"What are you talking about? What ability?" Lena asked confused.

"Your ability to make Kryptonite. My people could never get the formula quite right, so we had to steal or find it...but you, you can make it. Thanks to your formula so can we." Lillian said. As she spoke Lena saw the betrayed look on Supergirl's face and couldn't help the guilt rise in her.

"Lena would never hand it to you." Suupergirl said from the tank trying to sound defiant. Her faith in Lena making the younger Luthor's guilt intensify.

"I'm sure you thought she would never make Kryptonite, yet her we are." Lillian smiled. "But she doesn't need to give it to us, we have already taken it."

"So you were behind the hack?" Lena said.

"Of course we were." Lillian said. "I heard rumours of your achievements, but I didn't believe them until I saw the proof. For the first time since you were brought into my life I can honestly say I am proud of you." Lillian said, smiling a smile that made Lena's skin crawl.

"I grew out of needing your approval years ago." Lena replied.

"You've never needed it. But that doesn't mean you didn't crave it." Lillian said. "But this isn't about you. This is about Lex." Lillian said before turning to Kara. "Now we will learn what your limits are. After all I want to make your cousin's death as painful as possible."

"Stop this." Lena demanded.

"Now now Lena, after all your planning and stockpiling don't pretend you don't view them as the enemy." Lillian commented. "Don't worry you will be able to prove yourself."

"I don't want to prove myself to you." Lena said.

"You have a choice Lena, them or us." Lillian replied.

"What are you talking about?"

"In front of you are two buttons. Press the green one and the room that Supergirl is in will have the red lamps deactivated moments before it will be filled with Kryptonite gas, made from your Kryptonite. Press the red button and a bomb will detonate at the children's hospital."

"You can't do that." Lena said.

"I won't be. You will." Lillian said. "If you don't chose in sixty seconds both events will occur. But just to be clear if you press the green button there won't be time for the alien to escape before the Kryptonite fills the room."

"Press the green button." Kara said.

"It will kill you." Lena pointed out.

"Better me than the children." Kara argued.

"But-"

"Lena you have to. Press the green button." Kara pleaded.

"Twenty seconds." Lillian pointed out.

"I'm sorry." Lena said, shutting her eyes and pressing the green button.

"There is hope for you yet." Lillian said as green gas filled the room Kara was in. When Lena finally found the courage to open her eyes she saw Kara on her knees gasping for air as green gas surrounded her.

 **-TBC...**

* * *

 **A/N:** Thanks for reading and reviewing.


	3. Chapter 3

**A/N:** Thank you for the comments.

Guest (1) - I assume there will be a big discussion at some stage this season between Lena and Supergirl where they both air their grievances.

* * *

"That's enough." Lillian said after a couple of minutes watching Kara writhe. "Extract the gas and turn on the lamps." Turning she saw Lena's confused face. "This isn't about killing the alien. Not yet anyway. This is about learning so we can kill all Kryptonians and then all aliens. And you my daughter will help in my experiments. We'll start again in four hours, see if you can fix her."

For a moment Lena stood still, sickened by what she had done. But then her brain caught up and she said. "Wait. She'll heal quicker without the red light."

"I don't want her healed. Nor do I want her to escape. I just need her awake. The red lamps stay on." Lillian said before leaving.

Glaring at her mother's back Lena finally walked towards Kara's cell and stared at the guard until he unlocked the door and let her in.

"Kara?" Lena called as she entered the cell.

"Lena?" Kara wheezed. "You know?"

"I'm so sorry." Lena said dropping to her friend's side.

"No... Right call." Kara said still trying to breathe.

"What can I do?" Lena asked feeling helpless.

"Be...be my friend?" Kara asked, almost pleading.

"I am so sorry I let you down." Lena said as guilt consumed her. "Just rest I'll be here when you wake up." She added as Kara dropped unconscious.

-00-

"You can't go in there." A nurse protested as Alex barged into James's room.

"He's a friend and a witness." Alex said not slowing down.

"Alex?" James asked groggily.

"Where's Kara?" Alex asked.

"I don't know." James replied.

"Was she with you?" Alex pressed.

"Yes, no, not exactly...she was with Lena. I had their backs." James said shutting his eyes trying to recall what happened.

"No you didn't." Alex replied bluntly. "I need to know what happened."

"Ma'am, you can't be here. I will get security." The nurse interrupted.

"Then get security." Alex said before turning back to James. "What happened?"

"They were walking towards the meeting point, then nothing. They must have approached me from behind."

"How did you let that happen? What is the point of dressing like a tin man if you let them get to you?" Alex asked, her anger and concern running wild.

"Ma'am you need to leave now." A burly security guard said as he entered the room with his partner.

"Call me the second you remember something useful." Alex growled at James before leaving.

-00-

"Lena?" Kara asked when she woke.

"Kara." Lena said relieved. "How are you feeling?"

"Okay I guess." She said sitting up as she coughed before recalling the conversation earlier. "You called me Kara."

"Yes."

"You know."

"Yes."

"How long?"

"Awhile."

"I'm sorry." Kara apologised.

"Seeing I just gassed you with Kryptonite I think my betrayal is larger."

"You did what you had to do. What I asked you to do. It's not your fault." Kara said.

"How are you feeling?" Lena asked moving the conversation away from Kara trying to comfort her.

"Been better."

"I will get you out of this." Lena promised.

"How touching, but completely hollow." Lillian said over the speaker. "Only death will get her out of this and we have a lot of research to do before then." With that the guard opened the door and placed a bottle of water on the ground. Seeing her daughter's expression she said.

"Relax, it is just water. Drink some if you don't believe me. I need the alien to have some strength."

"Then turn off the red lamps." Lena said.

"Not happening. The best she can hope for is water. Take it or leave, it makes little difference to me." Lillian responded.

Cynically Lena picked up the bottle and drunk some of the contents. When she didn't feel any bad effects she looked at Kara.

"It didn't kill me, but it is from my mother. Do you want some?" When Kara nodded she put the bottle to Kara's lips. After taking a few sips Kara whispered her thanks and lay back down, her energy still gone.

"How are you feeling?" Lena probed. Before Kara answered her face scrunched in pain. "What's wrong?" Lena asked frowning.

"My stomach." Kara said clutching her gut.

"What's happening?" Lena asked staring back at her mother.

"You haven't figured it out? How disappointing." Lillian commented over the speaker system.

"What have you done?" Lena asked.

"Nothing. It was you who gave her the water." Lillian smiled.

"What have you done?" Lena repeated looking at the water bottle.

"I keep telling you, it's all you." Lillian said.

"You laced it with Kryptonite. You poisoned her." Lena guessed.

"Not quite." Lillian said smiling as Lena realised.

"I gave her water laced with Kryptointe. I poisoned her." With that she looked down at her friend, powerless to help and said. "Kara, I'm so sorry."

 **-TBC...**

* * *

 **A/N:** Thanks for reading and reviewing.


	4. Chapter 4

**A/N:** Thanks for your comments.

Guest (1) There will be lots of jumping to conclusions. But some will be more sway-able than others

* * *

"What have you found?" Alex asked as she stormed back into the control room.

"We managed to trace Kara's cell phone to approximately the same location as James Olsen was discovered a few hours ago." Brainy started.

"And?" Alex pressed.

"We dispatched a team to the location, but there was no sign of Supergirl. We did find Lena Luthor's cell phone, several foot prints and a couple of tyre marks. We have worked out the make and model of a van that was there last night." Vasquez explained. "Unfortunately there are several thousand registered in the city. Brainy is scanning CCTV footage."

"So we have nothing." Alex said despondently.

"Correct." Brainy yet before Vasquez tried to offer a comforting.

"Yet. We'll find her ma'am."

"Any news from J'onn?" Alex asked.

"Not yet ma'am." Vasquez replied.

-00-

As Kara once again threw up into a bucket Lena tried to soothe her as she held her hair out of the way.

"I'd offer water but that will only make it worse." Lena said apologetically.

"It's okay." Kara said collapsing back against the side of the cell.

"No it's not." Lena said angrily.

"You don't have to stay." Kara offered.

"Yes I do. You are like this because of me." Lena replied.

"Not your fault." Kara said.

Before Lena could respond the door opened and a guard slid a set of green cuffs towards her.

"Put them on her." Lillian ordered over the speakers.

"No." Lena said defiantly. "She needs water and to recharge her cells. Kryptonite could kill her."

"I doubt yet." Lillian said. "Put them on her."

"No." Lena responded.

"You always were the petulant child." Lillian recalled before asking. "Do you really hate children that much?"

"What are you talking about?" Lena asked.

"The bomb is still in place. If you don't do as I say it will be detonated."

"Do it." Kara said weakly holding out her arms.

Reluctantly Lena placed the cuffs on Kara and then looked to her mother.

"Time to move cells." Lillian said. "On your feet."

As Lena stood she watched Kara try to stand only to collapse to her knees. Stepping towards her friend she helped her to her feet and tried to support her weight.

"Clearly you have fed her too many potstickers." Lillian said snidely as she watched the struggle. "If you prefer the guards to drag her that is fine."

"I've got her." Lena said trying not to show the strain.

"Then follow the guards." Lillian said. "Oh, just in case you have any ideas of betrayal or escape those cuffs have bombs in. If you attempt to remove them without the correct code they will detonate killing both of you."

"Don't do anything stupid." Kara whispered as Lena helped her through the corridors.

"What are you talking about?" Lena asked.

"I can see you sizing up the guards in front. There is no way you can take them and the ones behind while I am like this."

"This could be our best chance." Lena said.

"Or it could get you killed." Kara countered.

"What about you?"

"I can hold on until Alex gets here." Kara said with so much conviction Lena nearly believed Alex would rescue them.

When they finally reached their destination the guard opened a metal door and directed Lena and Kara through it. As they entered Kara commented.

"At least there are no red lamps."

Before Lena could respond two guards approached and roughly took Kara from her before forcing her onto chair, which looked like a metal version of a dentist's chair. Ignoring Lena's protests they secured Kara to the chair before leaving, closing the door behind them.

"Now the real testing will begin." Lillian said over a speaker system. As she spoke a panel on the left of the room opened up. "On your left you can see a circuit. If it is not completed in the next three minutes the bomb will detonate. To complete the circuit correctly the circuit must be completed by something with the correct resistance. On the table to your right is a lead box. In it there is a syringe filled with Kryptonite. Take it and inject it into the alien." Lillian ordered.

"No." Lena replied defiantly.

"When you are done place the empty syringe in the circuit to your left." Lillian went on unperturbed by her daughter's out burst. "Once in the panel it will activate a circuit which will send a kill signal to the bomb at the hospital you went to last week. Attempt to put the syringe in with anything more than trace levels of kryptonite and the circuit will be destroyed and the kill signal won't be sent. If you attempt to mislead me in any way I will detonate the bombs in the cuffs and the hospital."

"No." Lena said.

"Have to." Kara said trying to be strong and not dwelling on the memories of Astra when she had undergone the same treatment.

"Tick, tock." Lillian said.

"Lena, you have to do this. If I had the strength to do it I would, but I don't and I know it is not fair to ask you to do this but you are the only chance those children have. Please do this."

"It will kill you." Lena said.

"No it won't. I've seen it done before. It won't kill me." Kara assured her.

With trembling hands Lena picked up the syringe and debated where to inject Kara to cause the minimal amount of pain. As if reading her thoughts Lillain's voice sounded round the room again and said.

"In the neck. Fifty seconds."

"Do it." Kara pleaded.

Reluctantly Lena pressed the syringe against Kara's neck and depressed the plunger, feeling sick as she saw Kara's face and neck show streaks of green as her friend screamed in agony. Once the syringe was empty she backed away and was so full of self hatred she nearly forgot to put the syringe in the circuit. Finally remembering what she had to do she completed the circuit and hoped her mother wasn't lying.

On the other side of the the two way mirror Lillian turned to one of her people and asked.

"Have you got yet?"

"Yes ma'am. It will be ready in less than ten minutes."

"Perfect."

 **-TBC...**

* * *

 **A/N:** Thanks for reading and reviewing.


	5. Chapter 5

**A/N:** Thanks for your comments.

Guest (1) - Lillian has a plan...

Alliedstatis - She will continue being slippery

* * *

"Anything?" Alex asked.

"No." Brainy said.

"Isn't there anything from the future you can use?" Alex asked, almost pleading.

"The future is not some sot of magic hat from which I can draw solutions on the utterings of some magic words." Brainy pointed out."And if there was a solution I would have used it."

"Director Danvers, you need to see this." A pale looking Vasquez said.

"What is it?" Alex asked, seeing Vasquez's face and feeling the panic rise within her.

"A video has just been uploaded by Cadmus. It is of Supergirl and Lena Luthor."

"Put it on the screen." Alex ordered.

Grimly nodding Vasquez did as she was ordered pulling up the video that started with the usual Cadmus message of hate and discrimination. The message then changed to proving that Supergirl was not a god. After that it showed Lena saying she had poisoned Supergirl with Kryptonite water before showing Supergirl lying on the ground clutching her stomach. Moments later the image switched to another room showing Supergirl clamped to a chair with Lena walking towards her holding a syringe. As it was injected into Kara's neck Alex saw the green glow and saw red.

"I will kill her." Alex ground out as she watched the video.

"We don't know all the facts yet." J'onn warned as he entered the control room.

"J'onn?" Alex said turning and hugging him.

"Sorry I took so long to get here." He apologised, hugging her tightly. He then added. "She's strong, we will find her."

"I know." Alex whispered into his chest.

"Good news." Brainy said.

"What?" Alex asked pulling away from J'onn.

"Supergirl is being tortured with Kryptonite." Brainy said.

"How is that good?" Alex almost shouted at him.

"It has a unique radiation signature, which I can track." He explained.

"I don't want to sound pessimistic, but Lillian will know that. They are probably in a lead lined room." J'onn pointed out.

"And you think that is a problem?" Brainy asked. Seeing their expressions he said. "Oh, you really think it is a problem. That is very twenty first century thinking."

"Brainy." Alex growled.

"Nothing completely blocks he radiation, just drastically reduces it. What is required is some simple signal processing, using a matched filter...I am surprised you were not able to do this before."

"Gloat later. Find her now." Alex said as she paced.

"Pacing is not conducive to working...but then again neither is you killing me. So I will just search." Brainy said rapidly typing at his work station.

After what felt like hours, but in reality was only minutes Brainy announced. "I have a location."

-00-

"Are you sure you don't want to wait for back up?" J'onn asked as he landed with Alex at the site Brainy had sent them to.

"You saw the video, who knows what they are doing to her." Alex said frowning.

"Let's go then. Stay behind me." J'onn instructed falling back into old habits. Ignoring Alex's quirked eyebrow he entered the building.

"Where is everyone?" Alex asked as she walked through the deserted building.

"Something isn't right." J'onn agreed.

"Brainy, are you sure you sent us to the right place?" Alex asked over the radio.

"Of course I'm sure." Brainy said.

"Then why is no one here?" Alex asked.

"According to the satellite imagery there was a mass exodus from that building twelve minutes ago." Brainy said after a minute.

"Twelve minutes?" Alex asked.

"Yes, just after I located them." Brainy confirmed.

"A mole or a leak, just what we need." Alex muttered before ordering. "Track the convoy that left." Before she could say anything else Alex and J'onn entered a dark room. Shining her flash light she saw a figure leaning over something. As her eyes focused she realised the figure was Lena and the thing she was leaning over was Kara.

"What have you done to her?" Alex almost screamed as she yanked Lena away from Kara and shoved her against the wall.

"Kryptonite." Lena said, the light too poor for Alex to see the haunted look on her eyes.

"Why? She was friend." Alex said anger taking over as she released Lena and ran to Kara.

"I'm here." She said to the unconscious body. "I'm taking you home." As she checked for obvious injuries she saw the Kryptonite cuffs and moved her hands towards them.

"You can't remove them. There are bombs in the cuffs." Lena said. "Take them off without the correct code and they'll explode. They'll kill Kara."

"You sick son of a-" Alex started only to bring her focus back to the more immediate problem and demanded. "What is the code?"

"I don't know."

"Bull." Alex said walking towards Lena. "What's the code?"

"I don't know." Lena said.

"What is the code?" Alex repeated aiming her gun at Lena.

"If I knew it I would have used it. My mother has it, she's the only one that knows it. But Brainy should be able to figure it out. She needs access to sun light."

"Alex." J'onn said placing a calming hand on her shoulder. "We have to get her back to the DEO."

For a moment Alex stood still before finally looking Lena in the eye and saying. "If she doesn't recover from this there will be no place on this planet that is safe for you."

"Alex." J'onn repeated making her step away from Lena. Turning Alex said.

"Take her back to the DEO, I'll meet you there."

Nodding J'onn scooped Kara up in his arms and flew off. Once he was gone Alex turned to Lena and said.

"The only reason you are still breathing right now is because you may have information that we need."

 **-TBC...**

* * *

 **A/N:** Thanks for reading and reviewing.


	6. Chapter 6

**A/N:** Thank you for the comments.

Guest (1) Brainy's skills will be used for something different.

Guest (2) Personally I think the whole market is saturated, especially when you bring in the movies. Adding another series risks making people so fed up of something they just switch off

Guest 3 - Right now I am just hoping they don't bring across any of the many, many, many plot holes of Batman Vs Superman

* * *

"How is she?" Alex asked rushing into the infirmary twenty minutes later.

"The Kryptonite cuffs have been removed. But it will be several hours before the Kryptonite is out of her system. Until then the best thing for her to do is sleep." Brainy explained.

"What about long term damage?" Alex asked.

"Too early to tell, but her cells are charging and her external injuries have healed." Brainy said. "I assumed you would want to check my work." He added handing her a tablet.

Silently she took the tablet and read the results for herself.

"Alex? Where are they?" James called limping towards her.

"Lena is in a holding cell. Kara is in the infirmary." Alex replied.

"Is Kara okay?" James asked.

"She was injected with Kryptonite. Of course she is not okay." Alex snapped.

"That really happened? Lena really did that?" James questioned, still not believing what he had seen.

"We haven't questioned her yet. But she didn't claim to be innocent." Alex replied.

"I want to be there when you question her." James said.

"Fine. But I need to see Kara first, you can meet me by the cells." Alex said. Not waiting for his reply she walked into the infirmary and straight to Kara's side.

"Hey." She said taking Kara's hand. "I'm sorry it took so long to find you. But you are safe now."

-00-

"Are you sure you want to do this?" J'onn asked as Alex approached the holding cells.

"I need to hear what happened." Alex said.

"I know. But now you are the Director you can't just lose it with a prisoner, especially a high profile one."

"I know." Alex said. "And I won't." Seeing J'onn's sceptical look she said. "Right now I feel like we are missing something. Lena holds the key."

"Missing what?" J'onn asked.

"No idea. Something just feels wrong. When Lillian is involved we normally jump to the wrong conclusions and let her get away. I'm not risking that this time."

"What can I do?" J'onn asked.

"Stay with Kara. Brainy said she won't be awake for a while, but just in case, I don't want her alone."

"I could question Lena while you stay with Kara." J'onn offered.

"I need to do this. I need to hear what happened. Don't worry, James will be in there with me."

"Okay." J'onn agreed, "But before you go in I think you missed something when we found them."

"Lena called Supergirl Kara." Alex said guessing what J'onn was referring to.

"Yes."

"I heard, I just didn't process it until an hour ago." Alex said. "That's another reason this doesn't feel right."

"If you need anything else jet me know. I'll sit with your sister."

-00-

"Why did you do it? Why inject her with Kryptonite? And why release the video?" Alex asked as she entered Lena's cell, James behind her.

"Video?" Lena asked confused.

"Yes the video of you torturing Supergirl." Alex said trying to control her anger. Seeing Lena's surprised expression she felt a glimmer of hope and said. "You didn't know there was a video. Was that video real? What happened?

"You're right I didn't know there was a video and I don't know what was on it. But I did torture Supergirl." Lena stated.

"Why? You are not evil." Alex said failing to comprehend what she was hearing.

"I did what I had to do." Lena said, her own guilt consuming her.

"Nothing needed you to inject her with Kryptonite." Alex said angrily.

"I don't know what you want me to say." Lena said. "I did it."

"You set this all up didn't you? Telling me about a meeting, was that even real? You knew I would ask Supergirl to go with you. It was all a trap. You really are like the rest of your family." James said walking out of room.

Not wanting to defend herself Lena merely fell silent.

"Why would you do that? That isn't you." Alex said.

"It doesn't matter why. All that matters is I am responsible for Kara being hurt." Lena said.

-00-

"Hey." Alex soothed when Kara opened her eyes.

"Alex?" She asked confused and disorientated.

"You're safe." Alex assured her. "It's over."

"Lena?"

"We've got her." Alex replied.

"Does she hate me?" Kara asked sadly. The question seemingly confirming Lena's involvement in Kara's torture.

"What happened was not your fault." Alex responded.

"No, it was." Kara argued as she tried to fight the weariness.

"Listen to me Kara. Nothing that happened was your fault. You need to rest, so get some sleep."

 **-TBC...**

* * *

 **A/N:** Thanks for reading and reviewing.


	7. Chapter 7

**A/N:** Thank you for the comments.

Chloe - Lena will be her own worst enemy for a couple of chapters.

Guest (1) - if they are bringing in Lex hopefully they will stop trying to turn Lena into him.

Guest (2) - To be honest I've given up to plan on writing anything specific.

* * *

"How's your sister?" J'onn asked as Alex approached him.

"Woke up briefly. She seemed more concerned about Lena than herself. Not even Kara would do that if things played out how we think they did."

"More went on than we are being told." J'onn agreed. "Releasing the video of what happened doesn't make sense. I mean showing it was Lena makes her a criminal. Why would she let that happen?"

"She didn't know about the video." Alex said.

"So she was set up?" J'onn guessed.

"Only we saw the video, we saw what happened. Lena said it was true. Kara also thought Lena hated her."

"But?"

"But it doesn't feel right. Lena and Supergirl may not have been getting on, but Lena is not evil and Kara is her best friend. She knew Kara was Supergirl. She knew hurting Supergirl was hurting her best friend. Plus she has continually fought against her mother. I feel like we are missing something."

"Do you want me to scan her mind?"

"No. Not yet. I want to try one more time."

-00-

"I still don't get it." Alex said entering Lena's cell. "You are not a bad person. The only reason you would do what you did is because you thought it was the right option. There were no traces of drugs in your system so you weren't hallucinating. So why do it?"

"I'm a Luthor." Lena said bitterly.

"Kara woke up." Alex threw in. The comment causing Lena to look up and ask.

"Is she okay?"

"She needs rest." Alex said. "But your reaction just now proves you do care. So what really happened?"

"You said you saw the video. You know everything that matters. I tortured, nearly killed Kara. I deserve to be locked away."

"I can't make you talk...well I probably can. At the very least I could get J'onn to read your mind. But I won't. Just answer one question."

"What?" Lena asked.

"Do you hate Kara?"

"No."

-00-

"Alex?" Kara asked seeing her sister by her side.

"Hey." Alex said jumping to her feet and grabbing hold of Kara's hand. "How are you feeling?"

"I hate Kryptonite. Why can't I have an Astra suit?"

"Brainy is working on one."

"He is?" Kara asked perking up.

"He is." Alex confirmed.

"Lena can probably help. She knows a lot about Kryptonite." Kara commented. Seeing Alex's frown she asked. "What? Is she not okay? She does hate me, doesn't she?"

"Lena is fine." Alex said.

"You promise?" Kara asked.

"I promise." Alex replied. "But if you are up for it I need you to tell me everything that happened."

"James told me Lillian had contacted Lena and was blackmailing her into meeting her. I didn't want her to go alone so when James told me where she was I went. She wasn't happy I was there. We were arguing about it and then I was shot by some Kryptonite darts. When I woke up I was in a clear cell with red lamps. Lena was unconscious outside." Kara recalled before falling silent.

"What happened then?" Alex prompted.

"It was bad." Kara said.

"I know, but I need to hear it."

"Okay, but I need you to know it was the only choice." Kara said.

"Okay." Alex agreed confused.

"When Lena woke up Lillian gave a choice. Press a green button and fill my tank with Kryptonite gas, or another button and set of a bomb at the children's hospital. I told her, begged her to hit the green button. She didn't want to, but she had no choice." Kara said shutting her eyes as she recalled what happened. As she did so she got lost in the memory and said. "I couldn't breathe, my skin burned, my eyes and throat were so painful. I thought that was it. Then it stopped."

"You are safe now." Alex assured her squeezing her hand. She then waited until Kara was able to go on. Eventually Kara said.

"The next few hours are fuzzy. Lena tried to help me, reassure me. She refused to leave my side. A guard put some water in the cell. She thought it was a trap so drunk some. She was fine and I was so thirsty after the gas so I asked for some...only it turned out it had Kryptonite in it. It was horrible."

"I'm so sorry I didn't get there sooner." Alex said as she tried to reconcile events in the video to what Kara was saying.

"I was so ill. Once again Lena refused to leave me alone. Once it was out of my system they threw some Kryptonite cuffs in the cell. Lillian threatened to explode the bomb if Lena didn't put them on me. After that I was moved to another room. Lena half carried me, I think it nearly killed her, but she didn't want the guards to drag me. Eventually we arrived at the new room and the guards tied me to a chair then locked us in the room. Lena was told to inject me with Kryptonite. If she didn't the bomb at the hospital would detonate. I thought if Astra could survive so could I. I just had to hold on until you found us. I couldn't inject myself, I was too weak so begged Lena to do it. She did but..."

"But what?" Alex asked.

"I knew it would hurt, but I never imagined how much. How could Lane do that to Aunt Astra? How could Lillian make her own daughter do that to anyone? Lena was in so much pain. How is she going to get over it?"

"I don't know." Alex said.

"Can I see her?" Kara asked after a few minutes of silence.

"You are not going anywhere." Alex said.

"She could come here." Kara suggested.

"Why did you think she hated you?" Alex asked.

"What?" Kara asked confused.

"Last time you were awake you asked if Lena hated you and earlier you asked again."

"She knows who I am." Kara said. "She knows I have been lying to her."

"She doesn't hate you. Get some rest. When you are sleeping I'll talk to Lena." Alex offered.

 **-TBC...**

* * *

 **A/N:** Thanks for reading and reviewing.


	8. Chapter 8

**A/N:** Thank you for the comments.

Guest (1) - It will be interesting to see what happens as Lena has recognised Lex as being completely insane. Maybe he'll just want to know what happened to his mansion.

* * *

"Kara is awake. She told me what happened." Alex said entering the cell. "Why didn't you tell me?"

"I did. I tortured her." Lena said.

"She told me everything. What happened in there, you didn't have a choice." Alex countered.

"There's always a choice." Lena said bitterly. "I made my choice when I made Kryptonite. Even if I hadn't been the one to inject her I still made the poison. As it was I chose to do both. And I know you well enough that regardless of the circumstances you still hold me responsible." Lena said.

"This isn't about me. This is about Kara and what Kara wants. And you have another choice to make." Alex said. "Kara wants to see you, she needs to see you. She thinks you hate her because she lied to you. So you can either sit here drowning in self pity or you can be the friend that Kara needs right now. Only you can make that choice." With that Alex turned and left the cell, leaving the door open.

-00-

"Lena? You're here?" Kara said surprised as Lena entered the infirmary.

"Would you like me to go?" Lena offered unable to look Kara in the eye.

"Of course not." Kara said trying to sit up.

"You probably shouldn't move." Lena said sensing Alex's disapproving glare from outside the room.

"Probably." Kara agreed finally sitting up. "I'm sorry."

"For what?"

"What happened."

"Why are you apologising? It was my mother that imprisoned you and me that tortured you." Lena pointed out still unable to look Kara in the eye. Reaching out Kara took Lena's hand and squeezed it.

"You did what I asked." Kara reminded her.

"If that were true I would have got rid of the Kryptonite months ago and this would have never happened."

"Pretty sure your mother would have found a way." Kara said. For a moment she said nothing, but finally she asked. "Why did you keep the Kryptonite?"

"I told myself it was to protect the Earth, in case there were more Worldkillers or more of Zod's or Non's armies. In part that was true, but maybe part of it was because I was hurt because you didn't trust me." Lena explained.

"Makes sense." Kara agreed.

"No it doesn't. I'm so sorry Kara." Lena said finally managing to make eye contact.

"I'm sorry too. I never should have lied."

-00-

"Here." Alex said handing Lena a glass of whiskey later that evening as Lena sat in an empty training room. As Lena looked suspiciously at the glass Alex added. "It's not poisoned. I wouldn't waste whiskey like that."

"What now?" Lena asked.

"You are free to go when you want. But you are not exactly popular in the City right now. I think you should stay here for safety."

"I deserve whatever happens." Lena said.

"There's only two people who can say that for sure. You and Kara. And Kara disagrees."

"Well she does have a knack of seeing the good when no one else can." Lena pointed out.

"Yes she does." Alex said. "She is definitely unique."

"Maybe not. Everyone accepted without question that I alone was responsible, except you." Lena said.

"I tried to kill you when we found you." Alex reminded her.

"After that, you questioned if I was responsible. No one, not even James, did. They were all happy to believe I was a Luthor."

"Well you didn't exactly defend yourself." Alex shrugged.

"Yet you kept questioning."

"Yeah, well I don't trust your mother. There are normally plenty of hidden agendas when she is around." Alex said. "But, you have shown us plenty of times that you are not evil. What you did din't make sense." Alex said. "Plus Kara has always believed in you."

"And I repaid that by making and stockpiling Kryptonite." Lena said bitterly. "Something that resulted in her torture. Torture that I was responsible for."

"We used to keep Kryptonite here. I shot Kara with a dart. I put her in a Kryptonite training room and punched her. I nearly killed her with a Kryptonite suit. It was our Kryptonite that your mother stole a couple of years ago." Alex explained. "I know what Kryptonite can do to her. How dangerous it is. How scared it makes her. But when we were fighting Reign I wanted an arsenal of Kryptonite. So I can't exactly lecture you on it. But if you want to help Kara and keep the world safe use your research to help Brainy make her a suit that neutralises the effects of Kryptonite." Alex said before pausing and changing direction.

"I get not feeling like you can confide in someone, not being able to ask for help. Ever since Kara came into my life I have been lying about something. But in all that time I've had Kara and then I had J'onn. But I remember how hard it was to trust and depend on him. So I understand why you hide things, but if you are going to remain friends with Kara, remain on the good side of grey that has to change. You have to let people in. You may be able to do everything by yourself, but there is a cost that comes with that attitude."

Knowing Lena needed time by herself Alex started to walk away only to add.

"She wanted to tell you who she was." Alex said. "The reason she didn't was to protect you. Your mother knew her identity and thought that you didn't. Kara was worried that if your mother thought you knew the truth she might come after you." Not waiting for a response Alex walked away.

-00-

"What are you doing?" Alex asked as she entered the infirmary and saw Kara moving around.

"Leaving. I'm all healed."

"Debatable." Alex said as she moved towards the scanners.

"Don't you have an agency to run?" Kara asked.

"Don't you have a traumatic experience to talk about?" Alex countered.

"I'm okay." Kara said.

"This is me you are talking to." Alex said.

"I've been where Lena was. I had a choice, save the Earth at the expense of Mon-El and the Daxamites or save Mon-El." Kara said. "I know that even though it was the right decision and if I had to do it again I would, it still hurts, it still haunts me. Lena did the right thing. She did what I asked, but nothing will take away the guilt. But the smallest thing will make her feel worse. I have to be strong for her."

"I get that. And that is part of what makes you you. But Lena isn't here right now. It is just you and me and it is okay to not be okay." Alex said. "So let me help you. What do you need?"

"A hug." Kara said meekly.

"Come on." Alex said pulling Kara into her arms.

As Kara clung to her sister she confessed. "I was so scared."

Not sure how to help Alex tightened her hold on her sister.

 **-TBC...**

* * *

 **A/N:** Thanks for reading and reviewing.


	9. Chapter 9

**A/N:** Thank you for the comments.

Guest (1) - If people become super villains after a bad day my conversion is way overdue. Lena, Kara and Alex will briefly address the Reign debate in the final chapter.

* * *

"Hello Kara, have you seen Alex?" Brainy asked as he entered the infirmary.

"She had to go to a meeting. Why?"

"No reason." He said.

"What's happened? Do you need Supergirl?" Kara asked sensing something had happened.

"No."

"Then what?"

"I wanted to give an update." Brainy said.

"About?" Kara probed.

"DEO matters."

"What are you hiding?" Kara asked suspiciously.

"Nothing."

"And I thought I was bad at lying." Kara commented.

"I should go." He said causing Kara to use her super speed and block the door.

"Why did you want to see Alex?" She pressed.

"I told you, DEO matters."

"What matters?" Kara pressed. "I'm not letting you leave until you tell me."

"Lena has decided to leave the DEO." He said.

"I have to stop her. It's not safe for her out there." Kara said turning.

"I should clarify. Lena has left the DEO." Brainy confessed.

"How did you let that happen?" Kara asked turning back to face him. "What else aren't you telling me?"

"As soon as her whereabouts were made public, the public attacked."

"Is she okay?" Kara asked eyes wide.

"For now. She is in her office at L-Corp. We have DEO agents keeping the building secure."

"I have to go." Kara said rushing out of the infirmary.

"Alex will not take this well." Brainy said.

-00-

"Kara? Are you okay? Should you be here?" James asked as Kara entered his office.

"I'm fine. And Supergirl is ready to make a statement...or give an interview. Which is better? Statement would be more controlled, but an interview will look more natural. It depends who does it though. Who is around right now?"

"Slow down. Does Alex know you are here?" James asked, losing track of what Kara was trying to say.

"Yes." Kara lied.

"What exactly do you want?"

"For Supergirl to give an interview about what happened."

"You don't have to do that." James said.

"Yes I do. So who is around? What about Spencer? He is always firm but fair." She said looking out into the ballpen.

"Um, yeah he's around." James said.

"Good, can you set up a TV interview in say ten minutes." She said before rushing out of the office.

"Kara, Kara wait." James called but she was already gone.

-00-

As Lena sat in her office at L-Corp she turned on the TV and watched reports of the attacks on her building with the captions 'Money and Corruption buys Freedom!' and 'Why is Lena Luthor Free?'

"That is a good question." She said out loud as she continued to channel hop. Just as she was about to turn the TV off the headline changed to, 'Breaking News: Supergirl Interview.'

Sitting up straighter she watched as Supergirl and Spencer appeared on the screen.

"Kara, what are you doing?" She asked as she watched the interview unfold.

"Supergirl, thank you for giving this interview. The first question I am sure everyone wants and answer to is, are you okay?" Spencer asked.

"I am." Supergirl nodded. "But I wanted to take this time to tell the world what happened. Many of you will have seen a video released on line of what happened when I was captured by Cadmus. However, the video was edited to give a misleading impression and to make you believe that the villain was Lena Luthor. That was not the case. The real villain was Lillian Luthor. Lena Luthor was an innocent party."

"You say the video was edited, but it clearly showed Lena Luthor injecting you with Kryptonite. Are you saying that didn't happen."

"It happened. But what the video didn't show you was why. There was a bomb at the Children's Hospital. If Lena had not injected me it would have exploded. Her actions saved the lives of hundreds of children as well as the doctors and nurses who flight to keep them healthy."

"So to be clear you are saying that Lena Luthor, the woman we all saw torture you is not responsible for what happened?"

"Yes."

"So you feel no ill-will towards Lena Luthor?"

"Absolutely none." Supergirl said. "Lena Luthor is a brave and independent woman who is not afraid to make the hard decisions despite the cost to her personally. She does not deserve the hatred that is being directed towards her. She deserves respect."

"Do you respect her?" He asked.

"I do. But in the past I have not given her all the respect she deserves. I hope I can correct that mistake in the future."

"Are you and Lena Luthor friends?" He probed, changing the direction of the interview.

"I would like to be." Supergirl replied.

"Oh Kara." Lena said looking at her screen. Before she could fully contemplate her words though, her phone rang. Looking down she saw the caller ID display James's name. Shaking her head she silenced the call.

 **-TBC...**

* * *

 **A/N:** Thanks for reading and reviewing.


	10. Chapter 10

**A/N:** Thank you for the comments.

Mikki - Thanks. I'm glad you are enjoying it.

Guest (1) - Two lessons that will never actually be learned.

Guest (2) - James was phoning to apologise in a too little too late way. The world may not react as you expect

Guest (3) - By the middle? That long? At least we (probably) now know why Lena makes a device to de-lead the atmosphere, it was actually to de-Kryptonite it (possibly).

* * *

"Alex? What are you doing here?" Kara asked as Alex entered her apartment.

"You were tortured. There is no way I'm letting you be by yourself tonight." Alex said. "Plus I need to yell at you for sneaking out of the DEO and then doing a press conference."

"I didn't really sneak, I flew straight out." Kara pointed out.

"Cute. I'm being serious Kara. Lillian is still out there and she has Kryptonite. She also knows who you are and we know she has a mole at the DEO. What is stopping her from coming here and taking you again?"

"You?" Kara suggested.

"Kara-" Alex started, her frustration building.

"I get it. I really do. But I am not the only target. She could come after you and she could come after Lena. I know you have my back, but who is looking after Lena."

"There is a DEO protection detail on her." Alex said.

"That's not the same as having a friend."

"I know." Alex said.

"Lena needs us right now."

Sighing Alex said. "I know. And I know Lena is your friend-"

"And yours." Kara pointed out. When Alex didn't immediately agree with what Kara had said Kara went on. "What Lena did, she had to do. You would have done the same. She needs her friends and you are one of her friends. If you can't do that for Lena, do it for me."

"Okay." Alex agreed. "But you will always be my priority."

"And I love you for it." Kara said. "But I had no control over what happened to me. I was powerless. But right now I am in a position to do something. Helping Lena will help me."

"You need to help yourself first." Alex warned.

"And who is looking after Lena?" Kara asked. "I heard what James said to her when she was at the DEO. Even if Lena can forgive him, can she trust him?"

"I don't know." Alex confessed.

"Lena needs us." Kara pressed.

-00-

"Kara? Alex? What are you doing here?" Lena asked as they entered her office.

"Alex won't let me be by myself and I won't let you be by yourself." Kara said.

"I'm fine." Lena said.

"No, you're not." Kara countered. "Secrets is what got us into this so how about we stop hiding things?"

"The only thing I am hiding is myself. If I go out there I endanger the protection detail you gave me."

"Technically that was Alex." Kara pointed out. "Why are you still in danger? I told everyone it wasn't your fault."

"They think I Stockholmed you." Lena said. "Until solid evidence is found of a bomb at the Children's hospital, with even stronger evidence that I had nothing to do with it they are not going to let up."

"It will take time." Alex agreed looking at Kara. "Just like it did with you after the Red-K."

"That's not fair. What happened isn't your fault." Kara said to Lena.

"You are pretty much the only one who believes that." Lena countered. "Which was probably my mother's plan all along."

"To what end?" Alex asked.

"I don't know. It could be anything from simple revenge to trying to make me turn to her side."

"That's stupid, you'd never do that." Kara said with no hint of doubt.

"You are literally the only person who believes that." Lena said. "Before I tarnish your reputation too, you should go."

"Not happening." Kara said.

"Kara-" Lena started.

"I know you feel betrayed by me right now and I don't deserve your friendship but-" Kara started.

"Kara, after what I did to you it shows that you were right not to confide in me." Lena said.

"You are going to blame yourself for what happened for a long time." Alex said to Lena, joining in the conversation. "And Kara is going to blame herself as that is what she does. So perhaps you two should just agree to start again, wipe the slate clean."

"I can do that." Kara said looking hopefully at Lena. In response the CEO nodded.

"Good, so we can have a proper girls' night." Kara said.

"I think there are more pressing concerns. Like my mother." Lena said.

"The DEO is looking for her." Kara pointed out. "The second they have a lead they will call me." Seeing the look Alex was giving her she corrected. "I mean they will call Alex. The point is we can't do anything right now. So why not watch a few movies?"

"You two are overdue a sisters' night." Lena said. "You should go."

"We are in this together." Kare said before turning to Alex with pleading eyes.

"I have whiskey." Alex pointed out. Seeing Kara's disapproving glare she asked. "What? You are ordering pizza." When Lena seemed unmoved Alex said. "Look at this way, spending time with us will annoy your mother more than anything else."

"That is a compelling argument." Lena agreed.

"So that's a yes?" Kara asked.

"That's a yes." Lena agreed. "But first there's something I have to do." Lena said standing and heading to her safe. Silently the sisters watched as she opened the lead safe and removed something. Locking the safe again she walked towards them and looked at Alex. "I've been thinking about what you said. I don't know if you are right, but your world sounded better than mine. When Sam came to me, I wanted to help my friend and I thought I was doing the right thing. It turned out I wasn't. I should have come to you both sooner. I should have trusted you both sooner."

"Well, I wasn't exactly blameless, I shouldn't have had James to spy on you." Kara said.

"Having seen what Kryptonite does to you I can see why you did it." Lena said. "If I had been honest from the start maybe we could have saved Sam sooner."

"Maybe." Kara said. "What I do know is we are stronger together."

"Yes we are." Lena said handing the hard disk form her safe to Alex.

"What's on it?" Alex asked.

"Everything. Including what my mother didn't get."

 **-The End**

* * *

 **A/N:** Thanks, for reading and reviewing. I hope you enjoyed it.


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